[petsc-dev] --download and spack

Sun Oct 21 16:37:05 CDT 2018

   Nope nothing to do with the PETSc module (which is perfect in every way ;-)). It is as Satish said, some old stuff in my ./spack/packages.yaml file that lied about the location of zlib.

   Barry

> On Oct 21, 2018, at 4:33 PM, Jed Brown <jed at jedbrown.org> wrote:
> 
> If I'm reading the error message correctly, isn't this a problem with
> the PETSc module for Spack (which you, Satish, and myself have
> contributed to), not with anything to do with Spack itself?
> 
> "Smith, Barry F." <bsmith at mcs.anl.gov> writes:
> 
>>   Needs some more work
>> 
>> 
>> ./bin/spack install petsc+hypre
>> ==> mpich at 3.2 : externally installed in /usr/local
>> ==> mpich at 3.2 : generating module file
>> ==> mpich at 3.2 : registering into DB
>> ==> zlib at 1.2.8 : externally installed in /usr
>> ==> zlib at 1.2.8 : generating module file
>> ==> zlib at 1.2.8 : registering into DB
>> ==> Installing hdf5
>> ==> Fetching https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.3/src/hdf5-1.10.3.tar.gz
>> ######################################################################## 100.0%
>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/hdf5-1.10.3-qe62ngz3szijov3frsc6sclbfylst3qk/hdf5-1.10.3.tar.gz
>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/hdf5-1.10.3-qe62ngz3szijov3frsc6sclbfylst3qk
>> ==> No patches needed for hdf5
>> ==> Building hdf5 [AutotoolsPackage]
>> ==> Executing phase: 'autoreconf'
>> ==> Executing phase: 'configure'
>> ==> Executing phase: 'build'
>> ==> Executing phase: 'install'
>> ==> Successfully installed hdf5
>>  Fetch: 4.37s.  Build: 2m 5.47s.  Total: 2m 9.84s.
>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/hdf5-1.10.3-qe62ngz3szijov3frsc6sclbfylst3qk
>> ==> Installing veclibfort
>> ==> Fetching https://github.com/mcg1969/vecLibFort/archive/0.4.2.tar.gz
>> ######################################################################## 100.0%
>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/veclibfort-0.4.2-jgzyxocuu54r2lqckfugttbk3gpvhthk/0.4.2.tar.gz
>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/veclibfort-0.4.2-jgzyxocuu54r2lqckfugttbk3gpvhthk
>> ==> No patches needed for veclibfort
>> ==> Building veclibfort [Package]
>> ==> Executing phase: 'install'
>> ==> Successfully installed veclibfort
>>  Fetch: 1.02s.  Build: 1.73s.  Total: 2.75s.
>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/veclibfort-0.4.2-jgzyxocuu54r2lqckfugttbk3gpvhthk
>> ==> Installing hypre
>> ==> Fetching https://github.com/LLNL/hypre/archive/v2.15.0.tar.gz
>> ######################################################################## 100.0%
>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/hypre-2.15.0-zzqagb6smd7uzznitrlvx3eor4oay3dg/v2.15.0.tar.gz
>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/hypre-2.15.0-zzqagb6smd7uzznitrlvx3eor4oay3dg
>> ==> No patches needed for hypre
>> ==> Building hypre [Package]
>> ==> Executing phase: 'install'
>> ==> Successfully installed hypre
>>  Fetch: 1.68s.  Build: 45.02s.  Total: 46.70s.
>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/hypre-2.15.0-zzqagb6smd7uzznitrlvx3eor4oay3dg
>> ==> cmake at 3.7.1 : externally installed in /usr/local/bin
>> ==> cmake at 3.7.1 : generating module file
>> ==> cmake at 3.7.1 : registering into DB
>> ==> Installing metis
>> ==> Fetching http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz
>> ######################################################################## 100.0%
>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/metis-5.1.0-x7k25qyuivjq4t4jb32gxagfa3qc4b3y/metis-5.1.0.tar.gz
>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/metis-5.1.0-x7k25qyuivjq4t4jb32gxagfa3qc4b3y
>> ==> Applied patch install_gklib_defs_rename.patch
>> ==> Ran patch() for metis
>> ==> Building metis [Package]
>> ==> Executing phase: 'install'
>> ==> Successfully installed metis
>>  Fetch: 3.86s.  Build: 8.33s.  Total: 12.19s.
>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/metis-5.1.0-x7k25qyuivjq4t4jb32gxagfa3qc4b3y
>> ==> Installing parmetis
>> ==> Fetching http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/parmetis-4.0.3.tar.gz
>> ######################################################################## 100.0%
>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/parmetis-4.0.3-st6cbngrj2r5jgtenru4f6jbtrbvhp3h/parmetis-4.0.3.tar.gz
>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/parmetis-4.0.3-st6cbngrj2r5jgtenru4f6jbtrbvhp3h
>> ==> Applied patch enable_external_metis.patch
>> ==> Applied patch pkg-parmetis-1c1a9fd0f408dc4d42c57f5c3ee6ace411eb222b.patch
>> ==> Applied patch pkg-parmetis-82409d68aa1d6cbc70740d0f35024aae17f7d5cb.patch
>> ==> Building parmetis [CMakePackage]
>> ==> Executing phase: 'cmake'
>> ==> Executing phase: 'build'
>> ==> Executing phase: 'install'
>> ==> Successfully installed parmetis
>>  Fetch: 3.71s.  Build: 8.08s.  Total: 11.79s.
>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/parmetis-4.0.3-st6cbngrj2r5jgtenru4f6jbtrbvhp3h
>> ==> python at 2.7.1 : externally installed in /usr
>> ==> python at 2.7.1 : generating module file
>> ==> python at 2.7.1 : registering into DB
>> ==> Installing superlu-dist
>> ==> Fetching https://github.com/xiaoyeli/superlu_dist/archive/v5.4.0.tar.gz
>> ######################################################################## 100.0%
>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/superlu-dist-5.4.0-zfeg63fl3jxidb2irxucgz7nvmintbzn/v5.4.0.tar.gz
>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/superlu-dist-5.4.0-zfeg63fl3jxidb2irxucgz7nvmintbzn
>> ==> No patches needed for superlu-dist
>> ==> Building superlu-dist [CMakePackage]
>> ==> Executing phase: 'cmake'
>> ==> Executing phase: 'build'
>> ==> Executing phase: 'install'
>> ==> Successfully installed superlu-dist
>>  Fetch: 2.03s.  Build: 22.54s.  Total: 24.57s.
>> [+] /Users/barrysmith/Src/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.0-apple/superlu-dist-5.4.0-zfeg63fl3jxidb2irxucgz7nvmintbzn
>> ==> Installing petsc
>> ==> Fetching http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.10.2.tar.gz
>> ######################################################################## 100.0%
>> ==> Staging archive: /Users/barrysmith/Src/spack/var/spack/stage/petsc-3.10.2-7fmmtqrr42secdvbosssdjc5lxnohh6b/petsc-3.10.2.tar.gz
>> ==> Created stage in /Users/barrysmith/Src/spack/var/spack/stage/petsc-3.10.2-7fmmtqrr42secdvbosssdjc5lxnohh6b
>> ==> No patches needed for petsc
>> ==> Building petsc [Package]
>> ==> Executing phase: 'install'
>> ==> Error: ProcessError: Command exited with status 2:
>>    'make' 'MAKE_NP=8'
>> 
>> 1 error found in build log:
>>     52    
>>     53    ==> 'make' 'MAKE_NP=8'
>>     54    makefile:15: lib/petsc/conf/petscvariables: No such file or directory
>>     55    makefile:16: /lib/petsc/conf/variables: No such file or directory
>>     56    makefile:17: /lib/petsc/conf/rules: No such file or directory
>>     57    makefile:18: /lib/petsc/conf/test.common: No such file or directory
>>>> 58    make: *** No rule to make target `/lib/petsc/conf/test.common'.  Stop.
>> 
>> See build log for details:
>>  /Users/barrysmith/Src/spack/var/spack/stage/petsc-3.10.2-7fmmtqrr42secdvbosssdjc5lxnohh6b/petsc-3.10.2/spack-build.out
>> 
>> Then in the build log
>> 
>> File "/private/var/folders/c1/ldz_dt8n2r3dtwv_chp5pfr40000gn/T/barrysmith/spack-stage/spack-stage-hFL0xI/petsc-3.10.2/config/BuildSystem/nargs.py", line 360, in setValue
>>    raise ValueError('Invalid directory: '+str(dir)+' for key '+str(self.key))
>> ===============================================================================
>>             Configuring PETSc to compile on your system                       
>> ===============================================================================
>> *******************************************************************************
>>                ERROR in COMMAND LINE ARGUMENT to ./configure 
>> -------------------------------------------------------------------------------
>> Invalid directory: /usr/include for key with-zlib-include
>> *******************************************************************************
>> 
>> 
>> Apple OS doesn't come with a /usr/include 
>> 
>> 
>>> On Oct 20, 2018, at 10:47 PM, Jed Brown <jed at jedbrown.org> wrote:
>>> 
>>> We're currently maintaining a (somewhat clumsy and limited, albeit
>>> functional) package manager in the form of the --download functionality.
>>> What do people think of outsourcing this to Spack, which would handle
>>> dependency resolution and report includes/libraries to PETSc?  That
>>> would enable reuse of installed packages between different PETSC_ARCH
>>> and be more reliable regarding upgrade/downgrade when switching
>>> branches.